General information for g643.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Ras association domain-containing protein 4.
Parent gene
- The parent gene g643 is located on chr_3: 4866962..4869576 (+ strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_3 | g643 | g643.t1 | TSS | g643.t1 | 4866670 | 4866670 |
| chr_3 | g643 | g643.t1 | isoform | g643.t1 | 4866962 | 4869576 |
| chr_3 | g643 | g643.t1 | exon | g643.t1.exon1 | 4866962 | 4867001 |
| chr_3 | g643 | g643.t1 | cds | g643.t1.CDS1 | 4866962 | 4867001 |
| chr_3 | g643 | g643.t1 | exon | g643.t1.exon2 | 4867055 | 4867533 |
| chr_3 | g643 | g643.t1 | cds | g643.t1.CDS2 | 4867055 | 4867533 |
| chr_3 | g643 | g643.t1 | exon | g643.t1.exon3 | 4867596 | 4868683 |
| chr_3 | g643 | g643.t1 | cds | g643.t1.CDS3 | 4867596 | 4868683 |
| chr_3 | g643 | g643.t1 | exon | g643.t1.exon4 | 4868745 | 4869071 |
| chr_3 | g643 | g643.t1 | cds | g643.t1.CDS4 | 4868745 | 4869071 |
| chr_3 | g643 | g643.t1 | exon | g643.t1.exon5 | 4869346 | 4869450 |
| chr_3 | g643 | g643.t1 | cds | g643.t1.CDS5 | 4869346 | 4869450 |
| chr_3 | g643 | g643.t1 | exon | g643.t1.exon6 | 4869516 | 4869576 |
| chr_3 | g643 | g643.t1 | cds | g643.t1.CDS6 | 4869516 | 4869576 |
| chr_3 | g643 | g643.t1 | TTS | g643.t1 | 4870342 | 4870342 |
Sequences
>g643.t1 Gene=g643 Length=2100
ATGTGGAAATGTAATAAATGTCAAAAACCTGTATATTTTGCTGAACGTCAACAAAGTCTT
GGTTTTGATTGGCATCCGGAATGTCTTCGATGTCATGAATGTGGAAAACGTCTTAATCCA
GGTCAGCATGCAGAACATAAAGGTGTGCCATATTGTCATGTACCTTGTTACGGTGCATTA
TTTGGGCCACAACTTTTTGGTCATGGAACTCGCGTTGAATCGCATAAAAGTTACGGACAA
AAGATCAACAATAGCATCGCATCACCAAAGAGCTCACCTGGACCAAACATTCCGCGCAAT
CATCTAGAATCTAAACTGAAAGTCTATAATAGTTTTTATAACAACAAGAGTCTCGAAATT
AAATCTCGCGAGGTGAATGGAAGATTCGTGCTCGAAGGCGCATTAAGGATTTATTGGGGT
ATACAAGGAGTGATTCATTTGAAAGAGGAAGATGATCAAAGAACTGTTGTTACCATTCGT
AAAAGAAATTCTGTTCGTTATCCCAATTCAGTTGATATTATAAGAGAAAGCAGCGTTTCA
GGATCTGATCAAGCGATTGTAGCTAGTGACAATGATACAACCATATCAGAATCGCTATCC
TATGACAATGTTAGTATCTCATCAGATATCAATTCTTTAGATTCAAGTGGATCATCAAAG
GAAAATTCACCATTACATGGAAGTAACACACTGCCCTCAAAATTAGATATCAAAAAAATT
GAATGGGACGATATTGATGAACTTTTGCAAGTAGAAAGAAAAAGTGATAATAATCACTAT
GCAACATTGCCATCTCCAATGACTTCCAGTATGACAGACAGCCAAATTTCAAATATCAGC
ACAGATGAATCAAGTTACAAAACTCTCTCACCTGATGGTGAAACAACTTCCGAATCATCA
AGTGTTTACTTCTCACAAATGGACTCAACAAATGCAGACAATAAACAAGTAAGCACAGAT
GACGATGATTCAACATTAAAGCCATGTGACTTTGAAGACTTTAAGCGACAAATCAGTCAG
GAATTTGTTAATGGTGCCAATGAATTGCCATCAATTAAAGATGGAACATTAAAACAAAAT
CAACCAATTGATCCGTCACGTATAAATGACTCGTTGAAACTTTATCAAGACAACATCATG
AATAGAAGTGTACAAAGTGAAGATGGATTAAGTGTTTATTCACTTTCAAATAGTTTCTGC
ATTCCTGGTCAAATTAATTCTTTTAATATTCAGGACACATTGAATTTATTAAAAAATTCT
TCATCTTCATCATCAGATGACAAAACGCTCAAACAAGAAAGCAATAAAGTGCTTAAAAAA
TCAAGTTCAATGAACTCATCAACATCTGAGGCAGATGATGACAACAGTTGGTCATCAGAC
AAGAAAATTTTACGATCAAAAAGTGGACCGAATTATGCTACAAATGATTTTGAAAGTGAA
ACAGTTAAGCCATCGAAAAAGCAGATGAAGCCAATTATAAATATTAAAATGGATTGTTAT
GATGAGCTCAAGAATGGATCATATGATGATGAAGGAACTGATCCAGTTATATTGAGGAAA
AAACAAAAAGGCTCAACGGCTATTAAAAGAAGATCGGGAAATCGAAGATCCCGAACAAAA
CTAAAACGCCGCTGTTCAATTAACGGTCACTTTTATAATCGTGAAACATCCATTTTTACA
CCACCAACTGGCTCACAAATGAGTGTTTATGCAACATCATTGCTCAATAGTCAGGAGATC
ATCAATTTAGTTATGGACAAATATAAAGTAGAATCAAAGGCTGAAAATTTTGCGCTTTTT
ATTGTGCGAGATAATGGCGAACAAAAGAAATTGACAAATGAAGATTATCCGTTAGTGACG
CGTGTATTGATGGGACCTCACGAAGATATTGCCCGTTTGTTTCTTATGGATGCTGGCTTA
GAGCCCGAAATTAGTCCTGAAGTCGCACAATTTGTCAATTTATCCATTCCTGAATGTCGA
TCAATAATTGAAAGATATTATGAAGAAGAAGAACGTGAATTGTTTAGAATTCGTGAAAAG
TATGCAGAATTCCGCAAAAGAATCATTCAACGAATGGAATCACTCAAAGTCAGATTGTAA
>g643.t1 Gene=g643 Length=699
MWKCNKCQKPVYFAERQQSLGFDWHPECLRCHECGKRLNPGQHAEHKGVPYCHVPCYGAL
FGPQLFGHGTRVESHKSYGQKINNSIASPKSSPGPNIPRNHLESKLKVYNSFYNNKSLEI
KSREVNGRFVLEGALRIYWGIQGVIHLKEEDDQRTVVTIRKRNSVRYPNSVDIIRESSVS
GSDQAIVASDNDTTISESLSYDNVSISSDINSLDSSGSSKENSPLHGSNTLPSKLDIKKI
EWDDIDELLQVERKSDNNHYATLPSPMTSSMTDSQISNISTDESSYKTLSPDGETTSESS
SVYFSQMDSTNADNKQVSTDDDDSTLKPCDFEDFKRQISQEFVNGANELPSIKDGTLKQN
QPIDPSRINDSLKLYQDNIMNRSVQSEDGLSVYSLSNSFCIPGQINSFNIQDTLNLLKNS
SSSSSDDKTLKQESNKVLKKSSSMNSSTSEADDDNSWSSDKKILRSKSGPNYATNDFESE
TVKPSKKQMKPIINIKMDCYDELKNGSYDDEGTDPVILRKKQKGSTAIKRRSGNRRSRTK
LKRRCSINGHFYNRETSIFTPPTGSQMSVYATSLLNSQEIINLVMDKYKVESKAENFALF
IVRDNGEQKKLTNEDYPLVTRVLMGPHEDIARLFLMDAGLEPEISPEVAQFVNLSIPECR
SIIERYYEEEERELFRIREKYAEFRKRIIQRMESLKVRL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g643.t1 | CDD | cd09401 | LIM_TLP_like | 4 | 57 | 6.19124E-31 |
| 13 | g643.t1 | CDD | cd01784 | RA_RASSF2_like | 553 | 638 | 5.41307E-38 |
| 12 | g643.t1 | Coils | Coil | Coil | 667 | 699 | - |
| 11 | g643.t1 | Gene3D | G3DSA:2.10.110.10 | Cysteine Rich Protein | 3 | 78 | 7.2E-19 |
| 10 | g643.t1 | Gene3D | G3DSA:3.10.20.90 | - | 525 | 638 | 4.7E-13 |
| 21 | g643.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 257 | 302 | - |
| 22 | g643.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 420 | 487 | - |
| 20 | g643.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 436 | 453 | - |
| 19 | g643.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 462 | 479 | - |
| 18 | g643.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 521 | 540 | - |
| 17 | g643.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 523 | 540 | - |
| 5 | g643.t1 | PANTHER | PTHR22738 | RASSF | 1 | 310 | 1.4E-158 |
| 7 | g643.t1 | PANTHER | PTHR22738:SF15 | LD40758P | 1 | 310 | 1.4E-158 |
| 4 | g643.t1 | PANTHER | PTHR22738 | RASSF | 418 | 699 | 1.4E-158 |
| 6 | g643.t1 | PANTHER | PTHR22738:SF15 | LD40758P | 418 | 699 | 1.4E-158 |
| 3 | g643.t1 | Pfam | PF00412 | LIM domain | 4 | 57 | 3.0E-11 |
| 2 | g643.t1 | Pfam | PF00788 | Ras association (RalGDS/AF-6) domain | 566 | 635 | 1.1E-6 |
| 1 | g643.t1 | Pfam | PF16517 | Novel Ras effector 1 C-terminal SARAH (Sav/Rassf/Hpo) domain | 655 | 692 | 2.8E-5 |
| 16 | g643.t1 | ProSitePatterns | PS00478 | LIM zinc-binding domain signature. | 4 | 38 | - |
| 23 | g643.t1 | ProSiteProfiles | PS50023 | LIM domain profile. | 2 | 63 | 13.365 |
| 25 | g643.t1 | ProSiteProfiles | PS50200 | Ras-associating (RA) domain profile. | 552 | 640 | 14.614 |
| 24 | g643.t1 | ProSiteProfiles | PS50951 | SARAH domain profile. | 648 | 695 | 12.808 |
| 15 | g643.t1 | SMART | SM00132 | lim_4 | 3 | 55 | 1.5E-12 |
| 8 | g643.t1 | SUPERFAMILY | SSF57716 | Glucocorticoid receptor-like (DNA-binding domain) | 3 | 29 | 1.85E-5 |
| 9 | g643.t1 | SUPERFAMILY | SSF57716 | Glucocorticoid receptor-like (DNA-binding domain) | 30 | 72 | 5.08E-11 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0007165 | signal transduction | BP |
KEGG
Orthology
- This transcript has been annotated with K09851 (Ras association domain-containing protein 2/4)
Pathway
- This transcript belongs to the following pathways
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.
